De novo assembly and annotation of Popillia japonica's genome with initial clues to its potential as an invasive pest.

BACKGROUND: The spread of Popillia japonica in non-native areas (USA, Canada, the Azores islands, Italy and Switzerland) poses a significant threat to agriculture and horticulture, as well as to endemic floral biodiversity, entailing that appropriate control measures must be taken to reduce its density and limit its further spread. In this context, the availability of a high quality genomic sequence for the species is liable to foster basic research on the ecology and evolution of the species, as well as on possible biotechnologically-oriented and genetically-informed control measures. RESULTS: The genomic sequence presented and described here is an improvement with respect to the available draft sequence in terms of completeness and contiguity, and includes structural and functional annotations. A comparative analysis of gene families of interest, related to the species ecology and potential for polyphagy and adaptability, revealed a contraction of gustatory receptor genes and a paralogous expansion of some subgroups/subfamilies of odorant receptors, ionotropic receptors and cytochrome P450s. CONCLUSIONS: The new genomic sequence as well as the comparative analyses data may provide a clue to explain the staggering invasive potential of the species and may serve to identify targets for potential biotechnological applications aimed at its control.

The direction, timing and demography of Popillia japonica (Coleoptera) invasion reconstructed using complete mitochondrial genomes.

The Japanese beetle Popillia japonica is a pest insect that feeds on hundreds of species of wild and cultivated plants including important fruit, vegetable, and field crops. Native to Japan, the pest has invaded large areas of the USA, Canada, the Azores (Portugal), Italy, and Ticino (Switzerland), and it is considered a priority for control in the European Union. We determined the complete mitochondrial genome sequence in 86 individuals covering the entire distribution of the species. Phylogenetic analysis supports a major division between South Japan and Central/North Japan, with invasive samples coming from the latter. The origin of invasive USA samples is incompatible, in terms of the timing of the event, with a single introduction, with multiple Japanese lineages having been introduced and one accounting for most of the population expansion locally. The origin of the two invasive European populations is compatible with two different invasions followed by minimal differentiation locally. Population analyses provide the possibility to estimate the rate of sequence change from the data and to date major invasion events. Demographic analysis identifies a population expansion followed by a period of contraction prior to the invasion. The present study adds a time and demographic dimension to available reconstructions.

3D renal model for surgical planning of partial nephrectomy: A way to improve surgical outcomes.

Objective: to evaluate the impact of 3D model for a comprehensive assessment of surgical planning and quality of partial nephrectomy (PN). Materials and methods: 195 patients with cT1-T2 renal mass scheduled for PN were enrolled in two groups: Study Group (n= 100), including patients referred to PN with revision of both 2D computed tomography (CT) imaging and 3D model; Control group (n= 95), including patients referred to PN with revision of 2D CT imaging. Overall, 20 individuals were switched to radical nephrectomy (RN). The primary outcome was the impact of 3D models-based surgical planning on Trifecta achievement (defined as the contemporary absence of positive surgical margin, major complications and ≤30% postoperative eGFR reduction). The secondary outcome was the impact of 3D models on surgical planning of PN. Multivariate logistic regressions were used to identify predictors of selective clamping and Trifecta's achievement in patients treated with PN (n=175). Results: Overall, 73 (80.2%) patients in Study group and 53 (63.1%) patients in Control group achieved the Trifecta (p=0.01). The preoperative plan of arterial clamping was recorded as clampless, main artery and selective in 22 (24.2%), 22 (24.2%) and 47 (51.6%) cases in Study group vs. 31 (36.9%), 46 (54.8%) and 7 (8.3%) cases in Control group, respectively (p<0.001). At multivariate logistic regressions, the use of 3D model was found to be independent predictor of both selective or super-selective clamping and Trifecta's achievement. Conclusion: 3D-guided approach to PN increase the adoption of selective clamping and better predict the achievement of Trifecta.

Novel Volumetric and Morphological Parameters Derived from Three-dimensional Virtual Modeling to Improve Comprehension of Tumor's Anatomy in Patients with Renal Cancer.

BACKGROUND: Three-dimensional (3D) models improve the comprehension of renal anatomy. OBJECTIVE: To evaluate the impact of novel 3D-derived parameters, to predict surgical outcomes after robot-assisted partial nephrectomy (RAPN). DESIGN, SETTING, AND PARTICIPANTS: Sixty-nine patients with cT1-T2 renal mass scheduled for RAPN were included. Three-dimensional virtual modeling was achieved from computed tomography. The following volumetric and morphological 3D parameters were calculated: VT (volume of the tumor); VT/VK (ratio between tumor volume and kidney volume); CSA3D (ie, contact surface area); UCS3D (contact to the urinary collecting system); Tumor-Artery3D: tumor's blood supply by tertiary segmental arteries (score = 1), secondary segmental artery (score = 2), or primary segmental/main renal artery (scoren = 3); ST (tumor's sphericity); ConvT (tumor's convexity); and Endophyticity3D (ratio between the CSA3D and the global tumor surface). INTERVENTION: RAPN with a 3D model. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Three-dimensional parameters were compared between patients with and without complications. Univariate logistic regression was used to predict overall complications and type of clamping; linear regression was used to predict operative time, warm ischemia time, and estimated blood loss. RESULTS AND LIMITATIONS: Overall, 11 (15%) individuals experienced overall complications (7.2% had Clavien ≥3 complications). Patients with urinary collecting system (UCS) involvement at 3D model (UCS3D = 2), tumor with blood supply by primary or secondary segmentary arteries (Tumor-Artery3D = 1 and 2), and high Endophyticity3D values had significantly higher rates of overall complications (all p ≤ 0.03). At univariate analysis, UCS3D, Tumor-Artery3D, and Endophyticity3D are significantly associated with overall complications; CSA3D and Endophyticity3D were associated with warm ischemia time; and CSA3D was associated with selective clamping (all p ≤ 0.03). Sample size and the lack of interobserver variability are the main limits. CONCLUSIONS: Three-dimensional modeling provides novel volumetric and morphological parameters to predict surgical outcomes after RAPN. PATIENT SUMMARY: Novel morphological and volumetric parameters can be derived from a three-dimensional model to describe surgical complexity of renal mass and to predict surgical outcomes after robot-assisted partial nephrectomy.

EZmito: a simple and fast tool for multiple mitogenome analyses.

Complete mitochondrial genome data are frequently applied to address phylogenetic/phylogeographic issues at different taxonomic levels in ecology and evolution. While sample preparation/sequencing is becoming more and more straightforward thanks to dropping costs for next-generation sequencing (NGS), data preparation and visualization remains a manually intensive step that may lead to errors if improperly conducted. We have elaborated, and here introduce, EZmito, a simple and intuitive, freely accessible Web Server aimed at automating some of these tasks. EZmito is divided into three main tools: EZpipe that assembles DNA matrices for phylo-mitogenomic analyses; EZskew that calculates genome, strand, and codon nucleotide compositional skews and EZcodon which computes Relative Synonymous Codon Usage statistics as well as amino acid usage frequency over multiple mitogenomes. Output is produced in tabular format as well as publication-quality graphics.

The robotic approach improves the outcomes of ERAS protocol after radical cystectomy: A prospective case-control analysis.

BACKGROUND: Minimally-invasive approach is one of the mainstays of Enhanced Recovery After Surgery (ERAS) pathways. Robot-assisted radical cystectomy (RARC) introduction has reduced the surgical burden on patient's recovery. Accordingly, ERAS protocol benefits may be more striking in RARC patients. We evaluated the impact of surgical approach on perioperative outcomes, Fast Track (FT) recovery steps and Trifecta success rates in patients undergoing RC followed by FT protocol. MATERIALS AND METHODS: We considered 147 patients who underwent RC, with open (Open radical cystectomy [ORC]; 47.6%) or robotic (RARC; 52.4%) approach at 2 tertiary centers. Urinary diversions were ileal conduit or orthotopic neobladder. All patients underwent FT protocol. We analyzed perioperative surgical and functional outcomes and Trifecta success rates (namely, defecation <5 days, in-hospital stay <10 days and no major complications). Uni and multivariable logistic regression explored the predictors for Trifecta success and the impact of surgical approach on recovery steps. RESULTS: Patients undergoing RARC had higher FT adherence (95% vs. 61%) compared to ORCs (P < 0.01). Trifecta success rates were higher for RARC (79.2% vs 28.6%; P < 0.001). At multivariable analyses, RARC was an independent predictor for Trifecta success (OR 9.1), early mobilization (OR 5.9) and FT adherence (OR 3.33; all P < 0.001). Surgical technique was not associated with major complications or readmission within 90 days (all P > 0.05). CONCLUSION: RARC has more favorable perioperative outcomes compared to ORC, with higher Trifecta success rates. Accordingly, robotic approach should be ideally included in every center where ERAS protocol is applied to RC for maximizing patient's recovery.

Interpreting nephrometry scores with three-dimensional virtual modelling for better planning of robotic partial nephrectomy and predicting complications.

OBJECTIVE: 3D models are increasingly used as additional preoperative tools for renal surgery. We aim to evaluate the impact of 3D renal models in the assessment of PADUA, RENAL, Contact Surface Area (CSA) and Arterial Based Complexity (ABC) for the prediction of complications after Robot assisted Partial Nephrectomy (RAPN). METHODS AND MATERIALS: Overall, 57 patients with T1 and 1 patient with T2 renal mass referred to RAPN, were prospectively enrolled. 3D virtual modelling was obtained from 2D computed tomography (CT). Two radiologists recorded PADUA2D, RENAL2D, CSA2D and ABC2D by evaluation of 2D images; two bioengineers recorded PADUA3D, RENAL3D, CSA3D and ABC3D by evaluation of the 3D model, using MeshMixer software. To evaluate the concordance between 2D and 3D nephrometry scores, Cohen's j coefficient was calculated. Receiver-operating characteristic (ROC) curves were generated to evaluate the accuracy of 3D and 2D nephrometry scores to predict overall complications. Finally, the impact of 3D model on clamping approach during RAPN was compared to 2D imaging. RESULTS: PADUA3D, RENAL3D, CSA3D and ABC3D scores had a significant different distribution compared to PADUA2D, RENAL2D, CSA2D and ABC2D (all p≤0.03). 2D nephrometry scores may be unchanged, reduced or increased after assessment by 3D models: CSA3D, PADUA3D, RENAL3D and ABC3D were reduced in14%, 26%, 29% and 16% and increased in 16%, 36%, 38% and 29% of cases, respectively. At ROC curve analysis, PADUA3D, RENAL3D and ABC3D showed were significantly better accuracy to predict complications compared to PADUA2D, RENAL2D and ABC2D. PADUA3D (OR: 1.66), RENAL3D (OR: 1.69) and ABC3D (OR: 2.44) revealed a significant correlation with postoperative complications (all P ≤0.03). CONCLUSION: Nephrometry scores calculated via 3D models predict complications after RAPN with higher accuracy than conventional 2D imaging.